Sat Oct 8 14:54:21 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 14:54:21 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6058544 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 27.94400 86.70399 ymin,ymax (A): 11.61800 64.67000 zmin,zma (A): 70.61500 117.7130 x,y,z range (A): 58.75999 53.05200 47.09800 scale (grids/A): 0.6058544 object centre (A): 57.32400 38.14400 94.16400 number of atom coordinates read : 3036 total number of charged atoms : 2888 net assigned charge : -3.485991 assigned positive charge : 454.8796 centred at (gu) : 89.95752 90.06701 89.82526 assigned negative charge : -458.3662 centred at (gu) : 90.03537 90.16011 89.73357 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7125 nv = 96 ne = 84 npr = 64935 no. pairs analyzed = 64935 no. exposed pairs = 3373 no. arc points = 23297 no. surface atoms = 1156 nbur = 1880 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 4155 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2288 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9036 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8354611E-09 2.7786498E-09 midg,1,midg; midg,igrid,midg 2.9204856E-09 -6.7462329E-09 1,midg,midg; igrid,midg,midg 2.2174207E-09 -5.7862057E-09 gauss-seidel spectral radius is 0.9859226 estimated iterations to convergence 69 setup time was (sec) 0.7000000 now iterating at: 14:54:22 rms-change max change #iterations 0.1289588 16.45679 at 10iterations 1.1320150E-02 1.487289 at 20iterations 1.0516879E-03 0.1614494 at 30iterations 1.0365971E-04 1.5506744E-02 at 40iterations 1.2669925E-05 1.8005371E-03 at 50iterations finished qdiffx linear iterations at : 14:54:26 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 1.2669925E-05 1.8005371E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 14:54:26 4.203u 0.240s 0:04.72 94.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 14:54:26 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.817563 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 27.94400 86.70399 ymin,ymax (A): 11.61800 64.67000 zmin,zma (A): 70.61500 117.7130 x,y,z range (A): 58.75999 53.05200 47.09800 scale (grids/A): 1.817563 object centre (A): 57.32400 38.14400 94.16400 number of atom coordinates read : 3036 total number of charged atoms : 2888 net assigned charge : -3.485991 assigned positive charge : 454.8796 centred at (gu) : 89.87202 90.20052 89.47498 assigned negative charge : -458.3662 centred at (gu) : 90.10567 90.48016 89.20078 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79028 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23297 grid for indexing accessible points = 1.400000 m= 26526 mr = 57159 m= 3223 mr = 19506 m= 126 mr = 1760 m= 0 mr = 39 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 30439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22630 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6058544 object centre at (A) : 57.32400 38.14400 94.16400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9091139E-03 1.0331828E-02 midg,1,midg; midg,igrid,midg -1.5140324E-02 -3.7956487E-02 1,midg,midg; igrid,midg,midg 1.0484922E-02 -2.6183270E-02 gauss-seidel spectral radius is 0.9985370 estimated iterations to convergence 207 setup time was (sec) 0.9900000 now iterating at: 14:54:27 rms-change max change #iterations 4.271638 171.6596 at 10iterations 1.941605 66.71635 at 20iterations 0.8861699 29.08615 at 30iterations 0.4053521 12.17768 at 40iterations 0.1860193 6.302037 at 50iterations 8.4846549E-02 2.522551 at 60iterations 3.8806904E-02 1.211061 at 70iterations 1.7739836E-02 0.5945454 at 80iterations 8.1319846E-03 0.2511544 at 90iterations 3.7221599E-03 0.1173221 at 100iterations 1.6986574E-03 5.4908752E-02 at 110iterations 7.8146881E-04 2.5089264E-02 at 120iterations finished qdiffx linear iterations at : 14:54:36 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 7.8146881E-04 2.5089264E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 14:54:36 9.610u 0.313s 0:10.20 97.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 14:54:36 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.726345 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 27.94400 86.70399 ymin,ymax (A): 11.61800 64.67000 zmin,zma (A): 70.61500 117.7130 x,y,z range (A): 58.75999 53.05200 47.09800 scale (grids/A): 2.726345 object centre (A): 57.32400 38.14400 94.16400 number of atom coordinates read : 3036 total number of charged atoms : 2888 net assigned charge : -3.485991 assigned positive charge : 454.8796 centred at (gu) : 89.80785 90.30070 89.21231 assigned negative charge : -458.3662 centred at (gu) : 90.15844 90.72026 88.80106 start vw surface at 0.1800000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 183675 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23297 grid for indexing accessible points = 1.400000 m= 89273 mr = 138553 m= 28357 mr = 73683 m= 5261 mr = 22336 m= 492 mr = 3653 m= 33 mr = 289 m= 0 mr = 9 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 68568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 23102 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.817563 object centre at (A) : 57.32400 38.14400 94.16400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2792049E-02 0.1057271 midg,1,midg; midg,igrid,midg -0.1988597 -0.3650154 1,midg,midg; igrid,midg,midg 0.1953366 -0.2060842 gauss-seidel spectral radius is 0.9992296 estimated iterations to convergence 284 setup time was (sec) 2.080000 now iterating at: 14:54:39 rms-change max change #iterations 10.10389 327.0984 at 10iterations 5.830540 134.0098 at 20iterations 3.338461 78.30408 at 30iterations 1.913891 39.88676 at 40iterations 1.091396 22.03935 at 50iterations 0.6213844 13.30536 at 60iterations 0.3546079 6.453057 at 70iterations 0.2022575 3.735487 at 80iterations 0.1150504 2.100821 at 90iterations 6.5571256E-02 1.179626 at 100iterations 3.7314404E-02 0.6729510 at 110iterations 2.1229060E-02 0.3914757 at 120iterations 1.2074010E-02 0.2068026 at 130iterations 6.8660257E-03 0.1320572 at 140iterations 3.9158673E-03 7.0858002E-02 at 150iterations 2.2385539E-03 4.0853024E-02 at 160iterations 1.2831445E-03 2.2028923E-02 at 170iterations 7.3817291E-04 1.4026523E-02 at 180iterations finished qdiffx linear iterations at : 14:54:53 total time elapsed so far: 15.94000 # loops : 180 mean,max change (kT/e) : 7.3817291E-04 1.4026523E-02 energy calculations done at 15.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.12000 DelPhi exited at 14:54:53 16.123u 0.311s 0:16.71 98.3% 0+0k 0+0io 0pf+0w